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Epigenomics
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Cell Reports - First Exon Length Controls Active Chromatin Signatures and Transcription

Cell Reports - First Exon Length Controls Active Chromatin Signatures and Transcription | Epigenomics | Scoop.it

Here, we explore the role of splicing in transcription, employing both genome-wide analysis of human ChIP-seq data and experimental manipulation of exon-intron organization in transgenic cell lines. We show that the activating histone modifications H3K4me3 and H3K9ac map specifically to first exon-intron boundaries. This is surprising, because these marks help recruit general transcription factors (GTFs) to promoters. In genes with long first exons, promoter-proximal levels of H3K4me3 and H3K9ac are greatly reduced; consequently, GTFs and RNA polymerase II are low at transcription start sites (TSSs) and exhibit a second, promoter-distal peak from which transcription also initiates. In contrast, short first exons lead to increased H3K4me3 and H3K9ac at promoters, higher expression levels, accuracy in TSS usage, and a lower frequency of antisense transcription. Therefore, first exon length is predictive for gene activity. Finally, splicing inhibition and intron deletion reduce H3K4me3 levels and transcriptional output. Thus, gene architecture and splicing determines transcription quantity and quality as well as chromatin signatures.

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Country-specific antibiotic use practices impact the human gut resistome

Despite increasing concerns over inappropriate use of antibiotics in medicine and food production, population-level resistance transfer into the human gut microbiota has not been demonstrated beyond individual case studies. To determine the "antibiotic resistance potential" for entire microbial communities, we employ metagenomic data and quantify the totality of known resistance genes in each community (its resistome) for 68 classes and subclasses of antibiotics. In 252 fecal metagenomes from three countries, we show that the most abundant resistance determinants are those for antibiotics also used in animals, and for antibiotics that have been available longer. Resistance genes are also more abundant in samples from Spain, Italy and France than from Denmark, the US, or Japan. Where comparable country-level data on antibiotic use in both humans and animals are available, differences in these statistics match the observed resistance potential differences. The results are robust over time as the antibiotic resistance determinants of individuals persist in the human gut flora for at least a year.

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DNA Methylation: an Epigenetic Aging Clock? - ScienceBlog.com (blog)

DNA Methylation: an Epigenetic Aging Clock? - ScienceBlog.com (blog) | Epigenomics | Scoop.it
DNA Methylation: an Epigenetic Aging Clock?
ScienceBlog.com (blog)
How does the body know how old it is? Our metabolisms change as we get older, even though our DNA doesn't change.
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2013 Genomics: The Era Beyond the Sequencing of the Human Genome: Francis Collins, Craig Venter, Eric Lander, et al.

2013 Genomics: The Era Beyond the Sequencing of the Human Genome: Francis Collins, Craig Venter, Eric Lander, et al. | Epigenomics | Scoop.it

Curator: Dr. Aviva Lev-Ari

 

One decade following the completion of the  Sequencing of the Human Genome – the field of Genomics, the discipline that has emerged as a result of project completion has FOUR sections: Comparative Genomics, Genome Sequencing and Annotation, Functional Genomics, and Translational Genomics.


Via Dr. Stefan Gruenwald
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Considering DNA Methylation and Aging

Considering DNA Methylation and Aging | Epigenomics | Scoop.it
An article on DNA methylation, which researchers have demonstrated to have the basis for a biomarker of aging; some of the patterns that tend to occur in the way in which these epigenetic decorations to DNA occur correlate ...
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Abstract | Epigenetics & chromatin: interactions and processes

On 11 to 13 March 2013, BioMed Central will be hosting its inaugural conference, Epigenetics & Chromatin: Interactions and Processes, at Harvard Medical School, Cambridge, MA, USA. Epigenetics & Chromatin has now ...
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Creative Approaches to Next-Gen Sequencing - Genetic Engineering News (blog)

Creative Approaches to Next-Gen Sequencing - Genetic Engineering News (blog) | Epigenomics | Scoop.it
Creative Approaches to Next-Gen Sequencing
Genetic Engineering News (blog)
With the tidal wave of next-generation sequencing sweeping through the landscape of biomedical sciences and technology, researchers are inundated with a flood of data.
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NGSANE: A Lightweight Production Informatics ... [Bioinformatics. 2014] - PubMed - NCBI

PubMed comprises more than 23 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
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PLOS ONE: DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing

PLOS ONE: DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing | Epigenomics | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
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DNA Methylation Rules: Studying Epigenetics with New Tools - Genetic Engineering News

DNA Methylation Rules: Studying Epigenetics with New Tools - Genetic Engineering News | Epigenomics | Scoop.it
Genetic Engineering News DNA Methylation Rules: Studying Epigenetics with New Tools Genetic Engineering News Cytosine hydroxymethylation (5-hydroxymethylcytosine, or 5hmC), the aforementioned DNA modification resulting from the enzymatic conversion...
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Shotgun DNA Methylation Bisulfite Sequencing Shows Male/Female ...

Shotgun DNA Methylation Bisulfite Sequencing Shows Male/Female ... | Epigenomics | Scoop.it
In a recent paper, researchers from Japan report that male and female primordial germ cells (PGCs) have different methylomes during development—at least in mice.
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More is not always merrier- methylation version. | Exploreable

More is not always merrier- methylation version. | Exploreable | Epigenomics | Scoop.it
Drugs like Azacitidine and Decitabine are passive hypomethylating agents – they are analogs of cytosine – one of the four bases that make up DNA, and react with DNA methyltransferase 1, which carries out DNA methylation ...
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Taking the gamble out of DNA sequencing | USC News

Two USC scientists have developed an algorithm that could help make DNA sequencing affordable enough for clinics — and could be useful to researchers of all stripes. Andrew Smith, a computational biologist at the USC ...
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Omics! Omics!: Post AGBT: A Longish Item on Long Sequencing

Omics! Omics!: Post AGBT: A Longish Item on Long Sequencing | Epigenomics | Scoop.it
As others have noted, a significant theme at AGBT this year was sequencing at length. While this year lacked true bombshells, PacBio impressed many with their making single-contig bacterial genome assemblies look easy.
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MGMT Methylation and Brain Tumors - UCSD Neurosurgery

MGMT Methylation and Brain Tumors - UCSD Neurosurgery | Epigenomics | Scoop.it
Methylation of DNA is a well known mechanism for controlling gene expression.
#Just_saying http://t.co/NB88xdcecx
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